[1] "Preparing Project:"
[1] "Hereeeeee"
[1] "Creating Object from..."
[1] "Patient data:"
[1] FALSE
[1] "Reading expression:tcga_coad_cms2.rds"
class: RangedSummarizedExperiment 
dim: 63856 144 
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
  ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(144): fb2cd7a6-c24c-4cfb-a508-5018c0952d36
  ee9a6aee-553c-40aa-a473-33c814d69636 ...
  2a0a7de1-ad34-408c-9ebf-f2ed2b8427f7
  0ca4170a-d922-4160-99b3-41baaaa8f4f7
colData names(937): rail_id external_id ... recount_seq_qc.errq
  BigWigURL
[1] "Map Barcodes..."
[1] "Normalize with CPM..."
[1] "LOG: There are 144 intial columns "
[1] "fb2cd7a6-c24c-4cfb-a508-5018c0952d36"
[2] "ee9a6aee-553c-40aa-a473-33c814d69636"
[3] "b4926f28-3fe4-4131-9b56-f160c24a3637"
[4] "223b5404-763f-4b7a-9942-54b79ed6d847"
[5] "294cb58f-4137-4680-af24-abff1d7a076e"
  [1] "TCGA-AA-A01F-01A-01R-A002-07" "TCGA-DM-A1DB-01A-11R-A155-07"
  [3] "TCGA-D5-5537-01A-21R-1928-07" "TCGA-AA-3534-01A-01R-0821-07"
  [5] "TCGA-QG-A5YV-01A-11R-A28H-07" "TCGA-AA-3989-01A-01R-1022-07"
  [7] "TCGA-G4-6306-01A-11R-1774-07" "TCGA-AA-3494-01A-01R-1410-07"
  [9] "TCGA-AA-3856-01A-01R-0905-07" "TCGA-CK-5912-01A-11R-1653-07"
 [11] "TCGA-A6-5662-11A-01R-1653-07" "TCGA-AA-3712-01A-21R-1723-07"
 [13] "TCGA-CM-6164-01A-11R-1653-07" "TCGA-AA-A02W-01A-01R-A00A-07"
 [15] "TCGA-A6-6652-01A-11R-1774-07" "TCGA-A6-5666-01A-01R-1653-07"
 [17] "TCGA-AA-3509-01A-01R-1410-07" "TCGA-CM-5864-01A-01R-1653-07"
 [19] "TCGA-A6-2677-01A-01R-0821-07" "TCGA-A6-5659-01B-04R-A277-07"
 [21] "TCGA-A6-5662-01A-01R-1653-07" "TCGA-A6-6140-01A-11R-1774-07"
 [23] "TCGA-AA-3693-01A-01R-0905-07" "TCGA-AA-A01I-01A-02R-A089-07"
 [25] "TCGA-DM-A1D0-01A-11R-A155-07" "TCGA-AA-3986-01A-02R-1022-07"
 [27] "TCGA-AA-A00Z-01A-01R-A002-07" "TCGA-CM-6677-01A-11R-1839-07"
 [29] "TCGA-AA-3841-01A-01R-0905-07" "TCGA-AA-3667-01A-01R-0905-07"
 [31] "TCGA-AA-3660-01A-01R-1723-07" "TCGA-A6-6648-01A-11R-1774-07"
 [33] "TCGA-AA-3524-01A-02R-0821-07" "TCGA-AA-3855-01A-01R-1022-07"
 [35] "TCGA-D5-6537-01A-11R-1723-07" "TCGA-CM-6166-01A-11R-1653-07"
 [37] "TCGA-G4-6294-01A-11R-1774-07" "TCGA-AA-3495-01A-01R-1410-07"
 [39] "TCGA-NH-A50T-01A-11R-A28H-07" "TCGA-AZ-6603-11A-02R-1839-07"
 [41] "TCGA-AA-3488-01A-01R-1410-07" "TCGA-AA-A017-01A-01R-A00A-07"
 [43] "TCGA-AA-3971-01A-01R-1022-07" "TCGA-AA-3831-01A-01R-0905-07"
 [45] "TCGA-F4-6808-01A-11R-1839-07" "TCGA-G4-6317-02A-11R-2066-07"
 [47] "TCGA-AA-3660-11A-01R-1723-07" "TCGA-G4-6307-01A-11R-1723-07"
 [49] "TCGA-AA-3844-01A-01R-1022-07" "TCGA-CM-4750-01A-01R-1410-07"
 [51] "TCGA-AA-3697-11A-01R-1723-07" "TCGA-A6-5659-11A-01R-1653-07"
 [53] "TCGA-CM-5862-01A-01R-1653-07" "TCGA-AA-3976-01A-01R-1022-07"
 [55] "TCGA-A6-6650-01A-11R-A278-07" "TCGA-AA-3562-01A-02R-0821-07"
 [57] "TCGA-DM-A282-01A-12R-A16W-07" "TCGA-A6-5656-01A-21R-1839-07"
 [59] "TCGA-A6-6138-01A-11R-1774-07" "TCGA-AA-3529-01A-02R-0821-07"
 [61] "TCGA-AA-3980-01A-02R-1022-07" "TCGA-AA-3970-01A-01R-1022-07"
 [63] "TCGA-AA-A01X-01A-21R-A083-07" "TCGA-AA-A02H-01A-01R-A089-07"
 [65] "TCGA-AD-6963-01A-11R-1928-07" "TCGA-A6-5656-01B-02R-A277-07"
 [67] "TCGA-AA-3519-01A-02R-0821-07" "TCGA-AD-6890-01A-11R-1928-07"
 [69] "TCGA-G4-6317-01A-11R-1723-07" "TCGA-AA-A01S-01A-21R-A083-07"
 [71] "TCGA-AA-3848-01A-01R-0905-07" "TCGA-CM-6676-01A-11R-1839-07"
 [73] "TCGA-AA-3509-01A-01R-1410-07" "TCGA-A6-5667-01A-21R-1723-07"
 [75] "TCGA-DM-A28H-01A-11R-A16W-07" "TCGA-A6-2677-01A-01R-A278-07"
 [77] "TCGA-AA-A01X-01A-21R-A083-07" "TCGA-A6-5659-01A-01R-1653-07"
 [79] "TCGA-AU-3779-01A-01R-1723-07" "TCGA-AA-3975-01A-01R-1022-07"
 [81] "TCGA-AA-3846-01A-01R-1022-07" "TCGA-CA-6716-01A-11R-1839-07"
 [83] "TCGA-AA-3688-01A-01R-0905-07" "TCGA-AA-A02F-01A-01R-A089-07"
 [85] "TCGA-AY-4071-01A-01R-1113-07" "TCGA-D5-5540-01A-01R-1653-07"
 [87] "TCGA-AA-3531-01A-01R-0821-07" "TCGA-AA-3955-01A-02R-1022-07"
 [89] "TCGA-AA-3542-01A-02R-1873-07" "TCGA-AA-3819-01A-01R-0905-07"
 [91] "TCGA-A6-2677-01B-02R-A277-07" "TCGA-AA-3972-01A-01R-1022-07"
 [93] "TCGA-A6-2680-11A-01R-A32Z-07" "TCGA-AA-3858-01A-01R-0905-07"
 [95] "TCGA-A6-2680-01A-01R-1410-07" "TCGA-AA-3534-11A-01R-A32Z-07"
 [97] "TCGA-AA-3552-01A-01R-0821-07" "TCGA-AA-3517-11A-01R-A32Z-07"
 [99] "TCGA-A6-A567-01A-31R-A28H-07" "TCGA-CA-5256-01A-01R-1410-07"
[101] "TCGA-AD-6888-01A-11R-1928-07" "TCGA-A6-5656-01A-21R-A278-07"
[103] "TCGA-AZ-6608-01A-11R-1839-07" "TCGA-AA-3712-11A-01R-1723-07"
[105] "TCGA-CM-6161-01A-11R-1653-07" "TCGA-AA-A00L-01A-01R-A002-07"
[107] "TCGA-AA-3979-01A-01R-1022-07" "TCGA-AA-3697-01A-01R-1723-07"
[109] "TCGA-AA-3679-01A-02R-0905-07" "TCGA-AA-3517-01A-01R-0821-07"
[111] "TCGA-D5-6532-01A-11R-1723-07" "TCGA-AA-3531-11A-01R-A32Z-07"
[113] "TCGA-G4-6626-01A-11R-1774-07" "TCGA-AA-A02J-01A-01R-A00A-07"
[115] "TCGA-AD-A5EK-01A-11R-A28H-07" "TCGA-A6-5660-01A-01R-1653-07"
[117] "TCGA-AA-3696-01A-01R-0905-07" "TCGA-CK-5915-01A-11R-1653-07"
[119] "TCGA-AA-3495-01A-01R-1410-07" "TCGA-CA-6715-01A-21R-1839-07"
[121] "TCGA-AA-A00Q-01A-01R-A002-07" "TCGA-D5-6533-01A-11R-1723-07"
[123] "TCGA-DM-A1D8-01A-11R-A155-07" "TCGA-A6-5667-11A-01R-1723-07"
[125] "TCGA-DM-A0XF-01A-11R-A155-07" "TCGA-CM-6678-01A-11R-1839-07"
[127] "TCGA-DM-A1D7-01A-11R-A155-07" "TCGA-CK-5914-01A-11R-1653-07"
[129] "TCGA-CA-5797-01A-01R-1653-07" "TCGA-G4-6298-01A-11R-1723-07"
[131] "TCGA-CA-5256-01A-01R-1410-07" "TCGA-AZ-6603-01A-11R-1839-07"
[133] "TCGA-AA-3678-01A-01R-0905-07" "TCGA-AD-6965-01A-11R-1928-07"
[135] "TCGA-A6-5659-01A-01R-A278-07" "TCGA-AA-A02K-01A-03R-A32Y-07"
[137] "TCGA-G4-6303-01A-11R-1774-07" "TCGA-AA-A00W-01A-01R-A002-07"
[139] "TCGA-A6-6650-01B-02R-A277-07" "TCGA-F4-6854-01A-11R-1928-07"
[141] "TCGA-A6-6650-01A-11R-1774-07" "TCGA-CM-6170-01A-11R-1653-07"
[143] "TCGA-AA-3561-01A-01R-0821-07" "TCGA-G4-6295-01A-11R-1723-07"
[1] "LOG: There are  mapped columns  "
[1] "LOG: There are 132 non duplicate samples "
[1] "Batch correction for  tcga.gdc_platform"
[1] "LOG: There are 20179 genes that pass mintpm filtering "
[1] "Using logcpm..."
[1] "WARNING: no purity for "
[1] "LOG: There are 132 samples that pass purity filtering "
[1] "Tissue type:  tumor  "
[1] "Get final data..."
[1] "Saving table..."
[1] "LOG: Table dimensions: 20179 x 121 "
[1] "DONE!"
[1] "Saving RDS..."
